Predicting Transcription Factor Affinities to DNA from a Biophysical Model

Supplementary Information

Helge Roider , Aditi Kanhere , Thomas Manke , Martin Vingron

• Binding matrix from Genome-Wide Location Analysis
  
  in vivo for 6870 yeast intergenic regions, 206 transcription factors
  from Harbison et al , Transcriptional regulatory code of a eukaryotic genome. Nature 431 , 99 (2004). download data
  
  in vitro for 6723 yeast intergenic regions, 3 transcription factors (Abf1,Rap1 and Mig1)
  from Mukherjee et al , Rapid Analysis of the DNA Binding Specificities of Transcription Factors with DNA Microarrays. Nature Genetics 36 , 1331 (2004). download data
  

• List of matrices for 25 transcription factors

• fasta file

• full table
• hits for every matrix and every intergenic region (balanced threshold)
• hits for every matrix and every intergenic region (type-I error threshold = 5%)

• download C source code for LINUX
  

  Compile: g++ TRAP.cpp -o TRAP 

  Usage:  TRAP   TRANSFAC_MATRIX  SEQUENCE_FILE  optional: Lambda and R0 

  Output: FASTA_ID  <N>  SEQUENCE_LENGTH